Polygenic Score (PGS) ID: PGS003773

Predicted Trait
Reported Trait HDL cholesterol
Mapped Trait(s) high density lipoprotein cholesterol measurement (EFO_0004612)
Released in PGS Catalog: Sept. 1, 2023
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Score Details

Score Construction
PGS Name HDL_AFR_CTSLEB
Development Method
Name CTSLEB
Parameters w_b= (50kb, 100kb), , clumping r2=(0.01, 0.05, 0.1, 0.2, 0.5, 0.8) , clumping window size = w_b/r2, p-value threshold = c(5E-08,5E-07,...,0.5,1), super leaner method was set to be glmnet and ridge to obtain linear weight
Variants
Original Genome Build GRCh37
Number of Variants 1,102,319
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000489
Citation (link to publication) Zhang H et al. Nat Genet (2023)
Ancestry Distribution
Source of Variant
Associations (GWAS)
Multi-ancestry (including European): 100%
  • European
  • African
  • Hispanic or Latin American
  • East Asian
  • South Asian
1,179,560 individuals (100%)
Score Development/Training
African: 100%
3,971 individuals (100%)
PGS Evaluation
African: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
Europe PMC: 34887591
 1,179,560 individuals European, African American or Afro-Caribbean, Hispanic or Latin American, East Asian, South Asian NR
Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
— 3,971 individuals,
42.0 % Male samples
 African American or Afro-Caribbean
(African American)		 UKB — Mean = 51.82 years
Sd = 8.06 years		 — — —

Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.

PGS Performance
Metric ID (PPM) 		PGS Sample Set ID
(PSS) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM018580 PSS011037|
African Ancestry|
3,983 individuals
 PGP000489 |
Zhang H et al. Nat Genet (2023)
 Reported Trait: High-density lipoprotein cholesterol — — R²: 0.09223 — —

Evaluated Samples

PGS Sample Set ID
(PSS) 		Phenotype Definitions and Methods Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS011037 — — 3,983 individuals,
42.0 % Male samples
 Mean = 51.82 years
Sd = 8.06 years		 African American or Afro-Caribbean
(African American)		 — UKB —